scverse

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49 repositories

squidpy_notebooks
Public
Tutorials for Squidpy
Jupyter Notebook
•
MIT License
•17•30•8•2•Updated Oct 31, 2024Oct 31, 2024
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•26•43•36•10•Updated Oct 30, 2024Oct 30, 2024
scverse.github.io
Public
scverse.org website
SCSS
•6•1•16•2•Updated Oct 30, 2024Oct 30, 2024
anndata
Public
Annotated data.
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
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BSD 3-Clause "New" or "Revised" License
•152•578•195•53•Updated Oct 30, 2024Oct 30, 2024
scvi-tools
Public
Deep probabilistic analysis of single-cell and spatial omics data
deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse
Python
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BSD 3-Clause "New" or "Revised" License
•350•1.2k•52•14•Updated Oct 30, 2024Oct 30, 2024
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
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BSD 3-Clause "New" or "Revised" License
•34•218•44•7•Updated Oct 30, 2024Oct 30, 2024
muon
Public
muon is a multimodal omics Python framework
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata
Python
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BSD 3-Clause "New" or "Revised" License
•30•215•36•3•Updated Oct 30, 2024Oct 30, 2024
scanpy
Public
Single-cell analysis in Python. Scales to >1M cells.
data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse python
Python
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BSD 3-Clause "New" or "Revised" License
•599•1.9k•504•74•Updated Oct 30, 2024Oct 30, 2024
squidpy
Public
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy
Python
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BSD 3-Clause "New" or "Revised" License
•79•434•61•6•Updated Oct 29, 2024Oct 29, 2024
pertpy-datasets
Public
Dataset preparation for pertpy
Jupyter Notebook
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MIT License
•1•1•1•0•Updated Oct 29, 2024Oct 29, 2024
rapids_singlecell
Public
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
bioinformatics gpu single-cell anndata scverse
Python
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MIT License
•21•147•11•4•Updated Oct 29, 2024Oct 29, 2024
ecosystem-packages
Public
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Python
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BSD 3-Clause "New" or "Revised" License
•40•19•6•6•Updated Oct 28, 2024Oct 28, 2024
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•0•1•0•Updated Oct 28, 2024Oct 28, 2024
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•9•69•19•1•Updated Oct 28, 2024Oct 28, 2024
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•115•186•15•3•Updated Oct 28, 2024Oct 28, 2024
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•12•11•13•5•Updated Oct 28, 2024Oct 28, 2024
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•13•35•55•7•Updated Oct 28, 2024Oct 28, 2024
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•17•38•6•4•Updated Oct 28, 2024Oct 28, 2024
scvi-tutorials
Public
Notebooks used in scvi-tools tutorials
scvi-tools scverse tutorial
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•25•46•8•5•Updated Oct 28, 2024Oct 28, 2024
simple-scvi
Public
Simple scVI implementation
Python
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BSD 3-Clause "New" or "Revised" License
•4•9•0•2•Updated Oct 28, 2024Oct 28, 2024
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•43•234•155•10•Updated Oct 28, 2024Oct 28, 2024
pytometry
Public
Flow & mass cytometry analytics.
Python
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Apache License 2.0
•10•42•12•1•Updated Oct 28, 2024Oct 28, 2024
napari-spatialdata
Public
Interactive visualization of spatial omics data
visualization spatial-analysis napari-plugin napari spatial-omics
Python
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BSD 3-Clause "New" or "Revised" License
•17•41•49•5•Updated Oct 28, 2024Oct 28, 2024
plotting_api
Public
Experimenting with a simplified plotting API for scanpy/scirpy
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•2•2•Updated Oct 28, 2024Oct 28, 2024
genomic-features
Public
Genomic Features in Python from BioConductor's AnnotationHub
genomics python
Python
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BSD 3-Clause "New" or "Revised" License
•5•19•19•7•Updated Oct 28, 2024Oct 28, 2024
pertpy
Public
Perturbation Analysis in the scverse ecosystem.
single-cell perturbation scverse
Python
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MIT License
•21•139•33•1•Updated Oct 26, 2024Oct 26, 2024
cookiecutter-scverse-instance
Public
Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.
Python
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BSD 3-Clause "New" or "Revised" License
•2•1•0•2•Updated Oct 25, 2024Oct 25, 2024
anndataR
Public
AnnData interoperability in R
anndata h5ad
R
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Other
•8•58•23•13•Updated Oct 24, 2024Oct 24, 2024
integration-testing
Public
A repo for integration testing core packages against upstream core packages
MIT License
•0•0•0•1•Updated Oct 18, 2024Oct 18, 2024
mudata
Public
Multimodal Data (.h5mu) implementation for Python
genomics muon data-analysis multi-omics anndata multimodal-omics-analysis mudata scverse
Python
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BSD 3-Clause "New" or "Revised" License
•17•77•12•1•Updated Oct 17, 2024Oct 17, 2024